Cheesy Baked Butternut Squash Mac and Cheese
Cheesy Baked Butternut Squash Mac and Cheese is not just your average comfort food; it’s a delightful spin on a classic dish that combines the creamy, cheesy goodness you love with the subtle sweetness of roasted butternut squash. This velvety mac and cheese is perfect for cozy family dinners or even as a potluck showstopper that will leave your friends and family asking for seconds (and thirds!). With its rich flavors and beautiful golden hue, this dish is as pleasing to the eyes as it is to the palate.
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I first stumbled upon this recipe during a chilly autumn afternoon, yearning for something warm and hearty. As I experimented in the kitchen, I realized that using butternut squash not only made the dish more colorful but also added an unexpected depth of flavor. Plus, it’s an easy way to sneak in some veggies that even picky eaters can’t resist. If you’re looking for a quick yet crowd-pleasing meal, this Cheesy Baked Butternut Squash Mac and Cheese is a must-try!
Why You’ll Love This Recipe
- Simple & Quick: Prep takes just 20 minutes, making this a perfect weeknight dish.
- Irresistible Flavor: The combination of sharp cheddar, Gruyere, and creamy butternut squash creates a flavor explosion.
- Eye-Catching Appeal: Its vibrant color and golden topping make it a showstopper at any gathering.
- Flexible Serving: Great for family dinners, potlucks, or a comforting snack.
- Diet-Friendly Options: Easily adaptable for dairy-free diets by substituting the cheese with your favorite alternatives.

Ingredients You’ll Need
- 1 large butternut squash: The star of the dish, it adds creaminess and a hint of sweetness. Look for one with a smooth, firm skin.
- 2 shallots, roughly chopped (⅔ cup): They offer a milder onion flavor that enhances the overall taste without overpowering it.
- 1 pound shell pasta: Shells, pipe rigate, or elbow pasta work great for holding onto the cheesy sauce.
- ¼ cup extra-virgin olive oil: Use good-quality olive oil for roasting the squash; it adds great flavor.
- 2 teaspoons balsamic vinegar: It gives a nice tang that balances the sweetness of the squash.
- 1½ teaspoons sea salt: Essential for enhancing all the flavors.
- 1 teaspoon onion powder: Adds an extra layer of onion flavor.
- ½ teaspoon garlic powder: A must-have for that comforting savory taste.
- ½ teaspoon ground sage: This herb complements the squash beautifully.
- ¼ teaspoon nutmeg: Just a pinch adds warmth to the dish.
- Freshly ground black pepper: For a finishing touch of spice.
- 1½ cups unsweetened almond milk: This keeps the dish creamy and light while being a great non-dairy option.
- 6 ounces grated sharp cheddar cheese (about 2½ cups): Provides a robust, tangy flavor that pairs perfectly with the creamy sauce.
- 6 ounces grated Gruyere cheese (about 2½ cups): This Swiss cheese adds a nutty depth and incredible meltiness.
- 1½ ounces finely grated pecorino cheese (½ cup): For an added kick of flavor many love; it can be substituted with Parmesan if needed.
- ¾ cup panko breadcrumbs: These give a delightful crunch to the topping.
- 1½ teaspoons extra-virgin olive oil: Just a touch for the breadcrumb topping, ensuring it gets nice and crispy.
How to Make Cheesy Baked Butternut Squash Mac and Cheese
Preheat the oven: Start by preheating your oven to 425°F. Line a baking sheet with parchment paper and grease a 9×13-inch baking dish to prevent sticking.
Prepare the squash and shallots: Slice the butternut squash in half lengthwise and scoop out the seeds. Drizzle the cut sides with 2 tablespoons of olive oil and season with salt and pepper. Place the squash cut side down on the baking sheet. For the shallots, place them on a piece of foil, add a drizzle of olive oil, sprinkle with salt, and wrap tightly. Place both the squash and shallots in the oven to roast for 30 to 45 minutes, until the squash is fork-tender.
Make the topping: While the squash is roasting, prepare the topping by mixing ¾ cup panko breadcrumbs with 1½ teaspoons of olive oil in a small bowl. This step is crucial for achieving that golden crispy top!
Cook the pasta: Bring a large pot of salted water to a boil. Add 1 pound of shell pasta, cooking according to package instructions until al dente. Reserve 1½ cups of the starchy pasta water before draining. This water will help bring your sauce together later.
Blend the squash sauce: After removing the roasted squash and shallots from the oven, measure out 2 cups of the cooked squash flesh and transfer it to a blender. Add the reserved pasta water, roasted shallots, ¼ cup olive oil, 2 teaspoons balsamic vinegar, 1½ teaspoons sea salt, 1 teaspoon onion powder, ½ teaspoon garlic powder, ½ teaspoon ground sage, ¼ teaspoon nutmeg, and a few grinds of pepper. Blend until creamy and smooth.
Combine pasta and sauce: In the same pot you cooked the pasta, heat 1½ cups of unsweetened almond milk over medium heat. Gradually stir in the blended squash sauce, cooking for about 3 minutes until warmed through. Whisk in the grated sharp cheddar, Gruyere, and pecorino cheeses, one at a time, ensuring each addition is completely melted before moving on. This creates a luxuriously creamy sauce.
Mix in the pasta: Once the cheese has melted into the sauce, add in the drained pasta and stir until it’s thoroughly coated. You’ll know it’s ready when it looks thick and luscious.
Broil the topping: Preheat your oven’s broiler, then transfer the creamy pasta mixture to the greased baking dish. Sprinkle the breadcrumb topping evenly over the mac and cheese. Broil for about 5 to 10 minutes, keeping a close eye until the topping is crispy and golden brown.
Cool before serving: Allow the dish to stand for about 15 minutes before digging in. This will help it set slightly and make serving easier.

Storing & Reheating
If you have any leftovers (which are rare!), allow the Cheesy Baked Butternut Squash Mac and Cheese to cool completely before transferring it to an airtight container. Store the dish in the refrigerator for up to 4 days. For longer storage, portion it into freezer-safe containers and freeze for up to 3 months. To reheat, simply thaw in the fridge overnight and heat in the oven at 350°F until warmed through, about 20 minutes. You may notice that the texture changes slightly after freezing, but a drizzle of almond milk while reheating can help refresh it.
Chef’s Helpful Tips
- When preparing the butternut squash, ensure it’s fully cooked and soft for the best blending results; undercooked squash can lead to a chunky sauce.
- Don’t rush the melting of the cheese; adding it gradually allows for a smoother sauce.
- To prevent gummy pasta, ensure you cook it al dente, as it will continue cooking while baking.
- For an extra flavor boost, try adding a dash of hot sauce or some chopped herbs like thyme or parsley to the cheese sauce.
- The recipe can easily be made ahead; simply follow the instructions and store it in the fridge before broiling right before serving.
Cheesy Baked Butternut Squash Mac and Cheese not only promises a delightful meal but also invites a warm gathering around the table. The unique combination of flavors and textures creates a wonderfully satisfying experience, making each bite a deliciously cheesy treat.
Experiment with different types of cheese or add-ins like spinach or cooked chicken for added layers of flavor. You’ll find that this recipe not only warms the heart but also leaves room for creativity in your cooking journey. We encourage you to relish every spoonful and share it with those you love.
Recipe FAQs
Can I use a different type of pasta?
Absolutely! While shell pasta is ideal for holding that gooey cheese sauce, you can easily substitute it with penne, rotini, or even gluten-free pasta if needed. Just follow package instructions for cooking times carefully!
Can I make this dish vegan?
Yes, you can! For a vegan version, substitute the cheese with a plant-based cheese alternative and use cashew or vegetable milk in place of almond milk. Nutritional yeast can also be a great way to add that cheesy flavor.
How can I add more vegetables to this dish?
Feel free to fold in steamed broccoli, spinach, or peas after mixing in your pasta and sauce. These additions not only boost nutrition but also add lovely color and texture to the dish!
Can I prepare this ahead of time?
Certainly! You can assemble the dish ahead of time, store it in the fridge, and then broil the topping when you’re ready to serve. This way, you’ll have a delicious, homemade meal ready to impress at a moment’s notice!
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📖 Recipe Card

Cheesy Baked Butternut Squash Mac and Cheese
- Prep Time: 20 minutes
- Cook Time: 80 minutes
- Total Time: 1 hour 40 minutes
- Yield: 8 servings 1x
- Category: Main Dishes
- Method: Baking
- Cuisine: American
Description
This Cheesy Baked Butternut Squash Mac and Cheese features a delightful blend of cheeses mixed with creamy butternut squash, making it a comforting dish that’s easy to prepare. It’s perfect for a cozy family dinner or a special gathering, appealing to all pasta lovers.
Ingredients
- 1 large butternut squash
- 2 shallots, roughly chopped (⅔ cup)
- 1 pound shell pasta, or pipe rigate or elbows
- ¼ cup extra-virgin olive oil, plus more for drizzling
- 2 teaspoons balsamic vinegar
- 1½ teaspoons sea salt
- 1 teaspoon onion powder
- ½ teaspoon garlic powder
- ½ teaspoon ground sage
- ¼ teaspoon nutmeg
- freshly ground black pepper
- 1½ cups unsweetened almond milk
- 6 ounces grated sharp cheddar cheese, about 2½ cups
- 6 ounces grated gruyere cheese, about 2½ cups
- 1½ ounces finely grated pecorino cheese, ½ cup
- ¾ cup panko breadcrumbs
- 1½ teaspoons extra-virgin olive oil
Instructions
- Preheat the oven to 425°F, line a baking sheet with parchment paper, and grease a 9×13-inch baking dish.
- Slice the squash in half lengthwise, scoop out the seeds, and drizzle the cut sides with olive oil. Sprinkle with salt and pepper, then place cut side down on the baking sheet.
- Wrap the shallots in foil with olive oil and salt. Add to the baking sheet and roast for 30 to 45 minutes until the squash is soft.
- For the topping, combine panko and olive oil in a small bowl and toss to mix well.
- Bring a large pot of salted water to a boil. Cook the pasta according to package instructions until al dente and reserve 1½ cups of the starchy pasta water before draining.
- In a blender, combine 2 cups of the cooked squash flesh, 1½ cups pasta water, shallots, olive oil, balsamic vinegar, salt, onion powder, garlic powder, sage, nutmeg, and pepper. Blend until smooth and creamy.
- In the same pot, heat the almond milk over medium heat. Gradually whisk in the squash sauce, cooking for three minutes until warmed throughout. Gradually add the cheeses, whisking until fully melted and the sauce is creamy. Stir in the pasta until well coated.
- Transfer the pasta to the prepared baking dish, top with panko, and broil for 5 to 10 minutes until crispy and browned.
- Let stand for 15 minutes before serving.
Notes
Feel free to use any pasta shape you prefer for this dish.
For added flavor, consider incorporating toasted nuts or herbs into the topping.
Nutrition
- Serving Size: 1 serving
- Calories: 490
- Sugar: 5g
- Sodium: 611mg
- Fat: 22g
- Saturated Fat: 4g
- Unsaturated Fat: 18g
- Trans Fat: 0g
- Carbohydrates: 62g
- Fiber: 5g
- Protein: 15g
- Cholesterol: 19mg
